User: frida

gravatar for frida
frida10
Reputation:
10
Status:
New User
Location:
rome
Last seen:
1 day, 15 hours ago
Joined:
4 months ago
Email:
o************@gmail.com

Posts by frida

<prev • 31 results • page 1 of 4 • next >
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Comment: C: Repetitive elements on my genome
... I have to find this option in help. Anyway, I'm interested in find the position in mygenome.fa that is divided in scaffold, not in query that is R=... ...
written 15 days ago by frida10
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Comment: C: Repetitive elements on my genome
... No i didn't. I can check it ...
written 15 days ago by frida10
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Comment: C: Repetitive elements on my genome
... I modified my post with some other information for better explain the problem ...
written 15 days ago by frida10
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Repetitive elements on my genome
... I'm analyzing mygenome.fa with RepeatScout and RepeatMasker to find transposable elements. I produced a library of Repetitive elements with repeatscout and the I masked TE using Repeatmasker. ``` ./build_lmer_table -l 14 -sequence mygenome.fa -freq mygenome.freq ./RepeatScout -sequence mygenome.fa ...
transposon written 15 days ago by frida10
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Comment: C: Pirate transposable elements pipeline
... Hi Smk, do you know repeatscout? If yes, can I ask you something about it? thank you ...
written 17 days ago by frida10
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Comment: C: Pirate transposable elements pipeline
... Thank you very much for your help!! I'll take a look to the review as soon as I can. :-) ...
written 19 days ago by frida10
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Pirate transposable elements pipeline
... hello, I'm doing an analysis of my unassembled genome of a specie of cephalopoda. I'm using repeatmasker but I'm interested to try others pipelines. I read something about Pirate here https://www.seanoe.org/data/00406/51795/. Does anyone know or has used it? Do you suggest me to use it? Thank you ...
transposable elements written 20 days ago by frida10 • updated 20 days ago by SMK380
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repeatscout installation: problem with filter stage
... I've installed Repeatscout in the cluster from https://bix.ucsd.edu/repeatscout/. I've also installed TRF and nseg required by the program. I followed the steps: ``` build_lmer_table -l 16 -sequence ~/file_fasta/od_1000.fa -freq od_1000.freq ``` ``` RepeatScout -sequence od_1000.fa -output od_10 ...
software error transposable elements written 23 days ago by frida10
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repeatscout: output l-mer table
... Hello everyone. I'm running Repeatscout. I built the l-mer table called myfile.freq of myfile.fa Can anyone tell me what do they mean the second and third columns produced as output? here I report an example: ``` AAAAAAAAGCGGGA 3 107776875 ``` ...
transposable elements genome table repeatscout written 25 days ago by frida10
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Comment: C: repeatmasker empty output
... Ok. In this repbase library I've found two .embl files with different types of TE. There are not fasta formats. Are they usable? The species in my analysis is an invertebrate (cephalopod) so what species shohld I use? Thank you again ...
written 4 weeks ago by frida10

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